Software in the HPC# 1. Module System 1.1. Where can I find installed software? 1.2. How can I find specific Python or R packages? 1.3. How can I find old software? 1.4. How can I find legacy software? 1.5. The toolchain of software packages 2. Graphical applications 2.1. X11 forwarding 2.2. Remote desktop sharing 3. Specific Use Cases 3.1. AlphaFold 3.2. Ansys Fluent 3.3. CESM/CIME 3.4. CP2K 3.5. GAMESS-US 3.6. GAP 3.7. Gaussian 3.8. GaussView 3.9. GROMACS 3.10. Mathematica 3.11. MATLAB 3.12. matplotlib 3.13. OpenFold 3.14. ORCA 3.15. PyTorch 3.16. R 3.17. SRA-Toolkit 3.18. Stata 4. Installing additional software 4.1. Compiling and testing your software on the HPC 4.2. Installing additional Python packages 4.3. Python virtual environments 4.4. Installing additional R packages 4.5. Installing additional Perl packages 4.6. Installing additional Julia packages